Author Archive

ChemSpider Mobile is a free iOS app (iPhone, iPod, iPad) for searching the ChemSpider online chemical database. It provides the ability to search by drawing a chemical structure, or entering a compound name. The app is very straightforward and easy to learn. Search results are shown in a list showing structure and names. Any search result can be examined in more detail by launching the mobile browser and viewing the structure on the ChemSpider web page.

Although the ChemSpider web page is designed to work well on mobile browsers, the mobile app is more convenient to use, and is currently the best way to search by structure from a mobile device. The structure drawing capabilities are provided by the embedded version of the Mobile Molecular DataSheet. The app was built by Molecular Materials Informatics, on behalf of the RSC.

RSC Publishing and its free database ChemSpider have integrated chemical semantic publishing across its chemical publications, and in collaboration with University of Manchester has made it accessible from the article PDF via the highly regarded Utopia Documents reader.

RSC Semantic Publishing

RSC has extracted chemical names from all its journal publications from 2008-2010 (over 30,000 articles), and has integrated the primary compounds of interest into ChemSpider. Readers of the article HTML on the RSC’s Publishing Platform can highlight compounds, and click on them to link directly through to ChemSpider’s compound record to discover additional data and compound information sources. The compounds will also shortly be visible from the article’s abstract page. Users of ChemSpider can discover these compounds via a text or structure search and, from a result, find the relevant references from RSC journal content and other integrated information sources. The project will run routinely on all new journal articles published by RSC and be extended further back into the RSC’s 170-year archive.

Integration with Utopia Documents

The free Utopia Documents reader can use this semantic information in the RSC’s enhanced articles to deliver this highlighting and linking functionality to RSC PDFs. Now readers of RSC PDF articles can use Utopia Documents to highlight and link from compounds directly through to ChemSpider and other information sources, thanks to the extension of Utopia by the software’s creators at The University of Manchester.

Richard Kidd, Informatics Manager at the RSC comments “expanding the integration of ChemSpider with our Publishing content, and applying routine semantic markup across ongoing and backfile content is a real milestone for how chemical science information can link together across the web. Being able to view all this through the PDF just makes it more accessible, and Utopia has continued to impress since it was first released.”

Steve Pettifer says, “Utopia Documents grew out of a need in the life sciences to regain some control of the mushrooming body of literature; it’s been really exciting for us to work with the RSC to expand into the field of chemistry and to bring our technology to a new audience.”

With this extension of semantic linking across our publications, RSC will now retire the use of the terms RSC Prospect & Project Prospect, used to describe the evolving project to enhance our articles which began back in 2007.

Both RSC and the Utopia Documents team are part of the Open PHACTS drug discovery consortium, which will be using the same technology to link disparate pharmacological data sources together under one view.

A new consortium of European organisations, including the RSC, unites to support next generation drug discovery by providing a single linked view across data sources, bringing the semantic web to drug discovery

The Open PHACTS consortium, funded by the Innovative Medicines Initiative, will reduce the barriers to drug discovery by applying semantic technologies to available data resources, creating an Open Pharmacological Space. The project runs from 2011-2014

The RSC’s role in the project will focus around its chemical data handling and integration experience provided by ChemSpider, and in its experience as a learned society publisher, to provide community engagement to support the project’s success.

Antony Williams, VP of Strategic Development, comments “It’s great to see the approaches that worked for ChemSpider offering a solution to wider data integration within Open PHACTS, and the RSC is delighted to form a part of such a high-quality consortium”

The RSC’s free chemical database ChemSpider has added RDF functionality to its interface, in collaboration with the University of Southampton’s School of Chemistry. The availability of RDF allows the database records to be found and understood by semantic web tools, another step in ChemSpider‘s mission to create a public chemical information infrastructure.

Richard Kidd, Informatics Manager at the RSC says “we are delighted to work with top academic teams pushing forward what’s possible with semantic chemistry, and we hope others will use the RDF representation of ChemSpider to support their own developments”

ChemSpider as a Linked Data source for oreChem

The machine-processable representation was specifically developed in order to leverage the core competencies of the ChemSpider database: resolvable identifiers; high-quality, curated metadata; and rich linking to the extensive RSC corpus. Furthermore, as part of the Microsoft Research-funded oreChem project, OAI-ORE technology is being used to facilitate the discovery and re-use of the chemical information in the correct context.

Prof Jeremy Frey and Dr Simon Coles commented “it is a pleasure for Southampton to work with the RSC’s ChemSpider as a culmination of our contribution to the Microsoft-funded oreChem project. As a member of the Southampton Chemistry eResearch team, this work forms the core of graduate student Mark Borkum’s PhD thesis. ”

“Enabling open, semantic chemistry in this way is a monumental step forward for the domain,” notes Lee Dirks, director of Education & Scholarly Communication for Microsoft Research, “We’re thrilled to have played a role in facilitating the creation of this resource and extremely pleased to see Southampton and the RSC innovating and leading the field.”

Another oreChem participant, Carl Lagoze, the Associate Professor, Cornell University Information Science, Co-Director Open Archives Initiative added “it’s wonderful to see the results of our work on OAI-ORE in this exciting application. It fulfils our goal of making the results of research easier to disseminate and reuse”

ChemSpider has been announced as the winner of the ALPSP Publishing Innovation award for 2010, and some of the team were present at the ALPSP Conference last Thursday as the envelope was opened. The judging panel commented that “[ChemSpider] has quickly become a highly valued and comprehensive community resource and has immense potential for future development”.

We’re especially proud as we were up against the other excellent shortlisted finalists of DataSalon’s Mastervision, the Semantic Biochemical Journal from Portland Press and the University of Manchester, and the AIP’s UniPHY social networking site.

We also managed to recreate the prize giving with Antony & Valery this morning – difficult to recreate the atmosphere of a conference dinner at 9am on an autumn Monday morning though…